SMTL ID : 6ck7.2 (1 other biounit)

Crystal structure of a peptide deformylase from Legionella pneumophila bound to actinonin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: Q.59, C.99, H.141, H.145 Ligands: BB2.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.99, A:H.141, A:H.145 ZN.5: 5 residues within 4Å: Chain B: Q.59, C.99, H.141, H.145 Ligands: BB2.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.99, B:H.141, B:H.145

2 x BB2: ACTINONIN(Non-covalent)

BB2.2: 19 residues within 4Å: Chain A: G.52, V.53, G.54, Q.59, E.96, E.97, G.98, C.99, L.100, Y.106, E.137, C.138, H.141, E.142, H.145 Chain B: E.96, Y.106 Ligands: ZN.1, BB2.6 15 PLIP interactions: 2 interactions with chain B, 13 interactions with chain A Hydrophobic interactions: B:E.96, B:Y.106, A:V.53, A:L.100, A:L.100, A:Y.106, A:H.141 Hydrogen bonds: A:V.53, A:G.54, A:Q.59, A:G.98, A:G.98, A:L.100, A:E.142 Water bridges: A:E.96 BB2.6: 20 residues within 4Å: Chain A: E.96, Y.106 Chain B: G.52, V.53, G.54, L.55, Q.59, E.96, E.97, G.98, C.99, L.100, Y.106, E.137, C.138, H.141, E.142, H.145 Ligands: BB2.2, ZN.5 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.53, B:L.100, B:L.100, B:Y.106, B:H.141, A:E.96, A:Y.106 Hydrogen bonds: B:V.53, B:G.54, B:Q.59, B:G.98, B:G.98, B:L.100, B:E.142 Water bridges: B:E.96

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 3 residues within 4Å: Chain A: K.169, R.172, R.176 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.176, A:R.176 Salt bridges: A:K.169, A:R.172, A:R.176 SO4.4: 3 residues within 4Å: Chain A: L.17, P.18, R.23 4 PLIP interactions: 4 interactions with chain A Water bridges: A:P.18, A:R.23, A:D.153 Salt bridges: A:R.23 SO4.7: 3 residues within 4Å: Chain B: K.169, R.172, R.176 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:K.169, B:R.172, B:R.176

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Edwards, T.E. et al., Crystal structure of a peptide deformylase from Legionella pneumophila bound to actinonin. To be Published

Release Date

2018-03-07

Peptides

Peptide deformylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Peptide deformylase

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